Sediment organic matter (SOM) is important in the biogeochemical cycling of carbon, nutrients, and pollutants in the coastal environment, which is increasingly disturbed by aquaculture that is particularly intense in China. However, the identification of aquaculture signals in SOM is rather challenging in the complex coastal environment that receives materials from a variety of sources. This was studied in a typical culture area of shellfish and algae in SE China from July 2019 to October 2020, using a combination of elemental (OC, TN, N/C), isotopic (δ¹³C and δ¹⁵N), spectral (absorption spectroscopy and fluorescence EEMs-PARAFAC), and statistical analysis (principal component analysis, PCA). All indices of SOM quantity and several spectral indices for the SOM composition correlated significantly with grain size, with lower SOM quantity and higher autochthonous contribution in coarse sediments. The strong correlations between elemental and spectral indices suggested that optical analysis could provide valuable indices for assessing the quantity of bulk organic matter. The comparison of SOM indices between different zones and between different months showed an overall limited influence of shellfish and laver culture. This indicated the sustainability of these types of aquaculture that require no manual addition of feeds and thus are generally clean. The further applications of end-member mixing analysis using the IsoSource program and PCA were more sensitive, which identified the removal of SOM by shellfish in the growing season and the contribution from shellfish residuals after the harvest and the cultured laver at some locations. Overall, our results have implications for a better understanding of the biogeochemical processes and ecosystem sustainability in the coastal environment under intense aquaculture activities.